In order to understand the mechanisms of coastal protection by salt marshes during typhoon events, in situ measurements of water level, tidal current speed and direction, and suspended sediment concentration (SSC) were carried out using Electromagnetic Current Meter (EMCM, AEM HR), miniature pressure sensor (MkV/D) and Seapoint Turbidity Meter (STM) sensor on a tidal flat in Quanzhou Bay, during the period when the typhoon “KAEMI” was passing through the region. The analysis of the data obtained shows that the near-bed current speed within the Spartina alterniflora marsh was generally below 5 cm s−1, which was apparently smaller than on the adjacent bare flat (i.e. 5–30 cm s−1). The change in the near-bed current speed in response to the typhoon event was not significant within the S. alterniflora marsh, but the current direction was influenced by the typhoon. The effect of the typhoon on the SSC was highly significant, with the SSC reaching 13 to 19 times the values on the bare flat or within the marsh under fair weather conditions; the near-bed SSC within the marsh was higher than on the bare flat, after the typhoon landed. The near-bed suspended sediment fluxes within the marsh and on the bare flat during the typhoon event were both enhanced, i.e., 4 times larger than under fair weather conditions. During the ebb, the bottom shear stress on the bare flat exceeded the critical shear stress for sediment motion for most of the ebb duration of the tide and, therefore, the bed sediment was eroding, with the erosion flux after the typhoon landed being around 2 to 3 times the value associated with fair weather conditions. In contrast, within the S. alterniflora marsh, the bottom shear stress was mostly lower than the critical shear stress for sediment motion, or lower than the critical shear stress for the maintenance of suspension; hence, the marsh surface was dominated by settling processes, with a settling flux during the typhoon being 3 to 6 times compared with the fair weather situations. The settling flux during the ebb was up to twice the magnitude for the flood. The comparison of sediment dynamic processes between the S. alterniflora marsh and the bare flat demonstrates that during the typhoon event the bare flat was dominated by erosion, whilst the presence of S. alterniflora favored the accretion of suspended sediment.